The Regulatory Genome

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Author: Eric H. Davidson
Publisher: Elsevier
ISBN: 9780080455570
Size: 69.43 MB
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The Regulatory Genome by Eric H. Davidson


Original Title: The Regulatory Genome

Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. The only book in the market that is solely devoted to the genomic regulatory code for animal development Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding Presents a comprehensive treatment of molecular control elements that determine the function of genes Provides a comparative treatment of development, based on principles rather than description of developmental processes Considers the evolutionary processes in terms of the structural properties of gene regulatory networks Includes 42 full-color descriptive figures and diagrams

Genomic Regulatory Systems

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Author: Eric H. Davidson
Publisher: Elsevier
ISBN: 9780080525594
Size: 57.37 MB
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Genomic Regulatory Systems by Eric H. Davidson


Original Title: Genomic Regulatory Systems

The interaction between biology and evolution has been the subject of great interest in recent years. Because evolution is such a highly debated topic, a biologically oriented discussion will appeal not only to scientists and biologists but also to the interested lay person. This topic will always be a subject of controversy and therefore any breaking information regarding it is of great interest. The author is a recognized expert in the field of developmental biology and has been instrumental in elucidating the relationship between biology and evolution. The study of evolution is of interest to many different kinds of people and Genomic Regulatory Systems: In Development and Evolution is written at a level that is very easy to read and understand even for the nonscientist. * Contents Include * Regulatory Hardwiring: A Brief Overview of the Genomic Control Apparatus and Its Causal Role in Development and Evolution * Inside the Cis-Regulatory Module: Control Logic and How the Regulatory Environment Is Transduced into Spatial Patterns of Gene Expression * Regulation of Direct Cell-Type Specification in Early Development * The Secret of the Bilaterians: Abstract Regulatory Design in Building Adult Body Parts * Changes That Make New Forms: Gene Regulatory Systems and the Evolution of Body Plans

Systems Biology And Regulatory Genomics

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Author: Eleazar Eskin
Publisher: Springer Science & Business Media
ISBN: 3540482938
Size: 45.27 MB
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Systems Biology And Regulatory Genomics by Eleazar Eskin


Original Title: Systems Biology And Regulatory Genomics

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.

Regulatory Genomics

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Author: Bogdan Tanasa
Publisher:
ISBN: 9781303457241
Size: 79.72 MB
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Regulatory Genomics by Bogdan Tanasa


Original Title: Regulatory Genomics

In the present dissertation, I integrate contemporary high-throughput sequencing (HT-seq) methods to characterize regulatory elements and transcriptional units in several biological systems in order to understand the molecular networks regulating the processes of gene expression. Our intense efforts contributed to several discoveries in biology, including a. the discovery of novel small RNA species that regulate mRNAs stability - the riRNAs, b. finding novel transcriptional units that regulate estrogen-dependent transcriptional events - the eRNAs, c. establishing the role of long noncoding RNAs in androgen-dependent gene expression - the lincRNAs PCGEM1 and PRNCR1, d. elucidating a novel epigenomics regulator - PHF8 as a H4K20me1 demethylase, e. characterizing a multifaceted transcrip- tional regulator - GPS2, f. identifying novel GWAS loci located in enhancers that carry disease susceptibility alleles. Chapter 1 reviews the current knowledge on genome regulatory elements, transcriptional units and chromatin architecture, and it describes 8 computational protocols that I have established in the laboratory for data analysis, together with their biological applications and methodological limitations. Chapter 2 details the use of HT-seq methods to characterize 2 novel transcriptional regulators (PHF8 and GPS2 ) that associate with promoters. Chapter 3 describes a novel small RNA species (riRNAs ), that derives from Alu retrotransposons and was bioin- formatically predicted to target the mRNAs. Chapter 4 describes the functions of enhancer RNAs in gene expression and chromatin interactions, by employ- ing GRO-seq and 3D-DSL methods. Chapter 5 describes 2 lincRNAs (PRNCR1, PCGEM1 ) that are over-expressed in prostate cancers and regulate tumor growth, by using ChIRP-seq and GRO-seq methods. Chapter 6 describes the biological functions of an enhancer in 9p21 gene desert, that carries genetic susceptibility to disease, and advances in 3D-DSL technology. I conclude with a section that summarizes these discoveries and outlines the potential areas of future research.

Computational Modeling Of Gene Regulatory Networks

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Author: Hamid Bolouri
Publisher: Imperial College Press
ISBN: 1848162200
Size: 58.82 MB
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Computational Modeling Of Gene Regulatory Networks by Hamid Bolouri


Original Title: Computational Modeling Of Gene Regulatory Networks

This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.

Epigenetic Gene Expression And Regulation

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Author: Suming Huang
Publisher: Academic Press
ISBN: 0128004711
Size: 59.81 MB
Format: PDF
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Epigenetic Gene Expression And Regulation by Suming Huang


Original Title: Epigenetic Gene Expression And Regulation

Epigenetic Gene Expression and Regulation reviews current knowledge on the heritable molecular mechanisms that regulate gene expression, contribute to disease susceptibility, and point to potential treatment in future therapies. The book shows how these heritable mechanisms allow individual cells to establish stable and unique patterns of gene expression that can be passed through cell divisions without DNA mutations, thereby establishing how different heritable patterns of gene regulation control cell differentiation and organogenesis, resulting in a distinct human organism with a variety of differing cellular functions and tissues. The work begins with basic biology, encompasses methods, cellular and tissue organization, topical issues in epigenetic evolution and environmental epigenesis, and lastly clinical disease discovery and treatment. Each highly illustrated chapter is organized to briefly summarize current research, provide appropriate pedagogical guidance, pertinent methods, relevant model organisms, and clinical examples. Reviews current knowledge on the heritable molecular mechanisms that regulate gene expression, contribute to disease susceptibility, and point to potential treatment in future therapies Helps readers understand how epigenetic marks are targeted, and to what extent transgenerational epigenetic changes are instilled and possibly passed onto offspring Chapters are replete with clinical examples to empower the basic biology with translational significance Offers more than 100 illustrations to distill key concepts and decipher complex science

Clinical Genomics

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Author: Shashikant Kulkarni
Publisher: Academic Press
ISBN: 0124051731
Size: 31.81 MB
Format: PDF, ePub
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Clinical Genomics by Shashikant Kulkarni


Original Title: Clinical Genomics

Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. This book is also focused on the challenges of diagnostic interpretation of NGS results in a clinical setting. Its final sections are devoted to the emerging regulatory issues that will govern clinical use of NGS, and reimbursement paradigms that will affect the way in which laboratory professionals get paid for the testing. Simplifies complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists towards genomic medicine paradigm Tried and tested practice-based analysis for precision diagnosis and treatment plans Specific pipelines and meta-analysis for full range of clinically important variants

Genomic Control Process

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Author: Isabelle Peter
Publisher: Academic Press
ISBN: 0124047467
Size: 66.40 MB
Format: PDF
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Genomic Control Process by Isabelle Peter


Original Title: Genomic Control Process

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Nutritional Genomics

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Author: Wayne R. Bidlack
Publisher: CRC Press
ISBN: 1439844534
Size: 46.72 MB
Format: PDF, ePub, Mobi
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Nutritional Genomics by Wayne R. Bidlack


Original Title: Nutritional Genomics

The notion of matching diet with an individual’s genetic makeup is transforming the way the public views nutrition as a means of managing health and preventing disease. To fulfill the promise of nutritional genomics, researchers are beginning to reconcile the diverse properties of dietary factors with our current knowledge of genome structure and gene function. What is emerging is a complex system of interactions that make the human genome exquisitely sensitive to our nutritional environment. Nutritional Genomics: The Impact of Dietary Regulation of Gene Function on Human Disease provides an integrated view of how genomic and epigenetic processes modulate the impact of dietary factors on health. Written as a resource for researchers, nutrition educators, and policy makers, this book contains the latest scientific findings on the mechanisms of action underlying diet-genome interactions. It presents a unique perspective on the fundamentals of nutritional genomics from genomics, transcriptomics, proteomics, and metabolomics. Contributing authors introduce the important areas of cell signaling and transduction, the intricate regulation of gene expression, and alteration of gene-linked chronic diseases, such as obesity-induced inflammation, insulin resistance, metabolic syndrome, cardiovascular disease, and cancer. The authors detail significant areas of interest within nutritional genomics—including plant-based foods as epigenetic modifiers of gene function and the effects of bioactive phytochemicals on inherited genotype and expressed phenotypes. They also discuss the role of vitamin D in various cancer risks and the gastrointestinal tract as a defense system. Given the key role played by agriculture and the food industry to produce foods to meet personalized health needs, the book also addresses agricultural breeding efforts to enhance nutritional value and the use of technology to increase bioactive ingredients in the food supply. The final chapters discuss manufacturing practices and novel processing techniques for retention of nutrients and bioactive components, as well as the need for regulatory oversight and proper labeling to establish assurance of safety and benefit. An excellent resource for this exciting field, the book identifies future directions for research and opportunities for improving global health and wellness by preventing, delaying, or mitigating chronic diseases with diet.

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